Deep Scientific Reasoning under Physical Constraints: Structure-Aware Spectrum Prediction

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

Simulating large molecular systems comprising thousands of atoms requires highly scalable methodologies. While modern Density Functional Theory (DFT) codes exhibit linear scaling, solving the associated large, sparse generalized eigenproblems remains a critical computational bottleneck on exascale architectures. In the context of the LimitX project, we propose a data-driven framework to accelerate these calculations. By shifting the machine learning target from discrete eigenvalues to the coefficients of an interpolating Chebyshev polynomial, and by comparing both all-atom and fragment-based structural representations, we successfully overcome the dimensionality constraints of large-scale spectral prediction. We investigate three machine learning models (Kernel Ridge Regression, Graph Neural Networks, and Random Forests) trained on a novel 2 TB dataset of protein dimers. The predicted spectra provide initial guesses that effectively bypass early Self-Consistent Field (SCF) iterations in BigDFT. Ultimately, these spectral predictors will be deployed to dynamically optimize upcoming rational filter-based eigensolvers, such as FrASE, which is currently in initial development.

Elucidating molecular structures from spectra is a foundational problem in chemical and materials characterization, yet remains challenging due to spectral ambiguity and the vast molecular space. Although recent diffusion-based generators show strong promise for spectra-conditioned elucidation, existing methods struggle to learn robust spectra-structure relationships from limited paired data when relying solely on global spectral representation. Moreover, the repeated full sampling inference strategy incurs substantial computation overhead. To address these limitations, we propose MAST, a Motif-Augmented diffusion framework with Search Tree, for joint 2D-3D spectroscopic molecular structure elucidation. MAST introduces explicit, interpretable motif priors as intermediate evidences throughout denoising, reducing conditional ambiguity and facilitating spectra-conditioned optimization. We further cast diffusion sampling as reward-guided tree search to prioritize high-reward denoising trajectories, yielding a compact set of spectra-consistent candidates under limited budgets. On the QM9S multi-spectra benchmark, MAST achieves 94.89% exact recovery and improves 3D fidelity, while preserving high chemical validity and stability. Code is available at https://github.com/Jia040223/MAST.